The aerodynamic performance of lifting surfaces operating at low Reynolds number conditions is impaired by laminar separation. In most cases, transition to turbulence occurs in the separated shear layer as a result of a series of strong hydrodynamic instability mechanisms. Although the understanding of these mechanisms has been significantly advanced over the past decades, key questions remain unanswered about the influence of external factors such as free-stream turbulence (FST) and others on transition and separation. The present study is driven by the need for more accurate predictions of separation and transition phenomena in ‘real world’ applications, where elevated levels of FST can play a significant role (e.g. turbomachinery). Numerical investigations have become an integral part in the effort to enhance our understanding of the intricate interactions between separation and transition. Due to the development of advanced numerical methods and the increase in the performance of supercomputers with parallel architecture, it has become feasible for low Reynolds number application ($O(10^{5})$) to carry out direct numerical simulations (DNS) such that all relevant spatial and temporal scales are resolved without the use of turbulence modelling. Because the employed high-order accurate DNS are characterized by very low levels of background noise, they lend themselves to transition research where the amplification of small disturbances, sometimes even growing from numerical round-off, can be examined in great detail. When comparing results from DNS and experiment, however, it is beneficial, if not necessary, to increase the background disturbance levels in the DNS to levels that are typical for the experiment. For the current work, a numerical model that emulates a realistic free-stream turbulent environment was adapted and implemented into an existing Navier–Stokes code based on a vorticity–velocity formulation. The role FST plays in the transition process was then investigated for a laminar separation bubble forming on a flat plate. FST was shown to cause the formation of the well-known Klebanoff mode that is represented by streamwise-elongated streaks inside the boundary layer. Increasing the FST levels led to accelerated transition, a reduction in bubble size and better agreement with the experiments. Moreover, the stage of linear disturbance growth due to the inviscid shear-layer instability was found to not be ‘bypassed’.